Research workbench
Structure of ampk bound to activator
Analyse Structure of ampk bound to activator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E4W
- Type
- protein
- Length
- 799 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-AMP-activated protein kinase catalytic subunit alpha-1; 5'-AMP-activated protein…
- EC
- 2.7.11.1, 2.7.11.27, 2.7.11.31, 2.7.11.26
- UniProt
- P54645, P80386, P80385
- Ligands
- AMP, STU, HUG, ADP, CL, SO4
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-AMP-activated protein kinase catalytic subunit alpha-1 (EC 2.7.11.1, 2.7.11.27, 2.7.11.31, 2.7.11.26) | protein | 362 | 34% helix, 23% strand | P54645 |
| B | 5'-AMP-activated protein kinase subunit beta-1 | protein | 159 | 14% helix, 45% strand | P80386 |
| C | 5'-AMP-activated protein kinase subunit gamma-1 | protein | 278 | 40% helix, 24% strand | P80385 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains C
- STU · Staurosporine · ligand · chains A
- HUG · 1-O-(4,6-difluoro-5-{4-[(2S)-oxan-2-yl]phenyl}-1H-indole-3-carbonyl)-beta-D-glucopyranuronic acid · ligand · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · chains C
- CL · Chloride ion · ion · 3 copies · chains A
- SO4 · Sulfate ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1055 | 0.78 | 0.80 | 91 | AMP, ADP, SO4 |
| 2 | 229 | 0.66 | 0.84 | 30 | STU |
| 3 | 205 | 0.59 | 0.81 | 26 | HUG |
| 4 | 318 | 0.58 | 0.77 | 31 | empty |
| 5 | 173 | 0.54 | 0.80 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2983 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 1174 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 386 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6E4W · Structure of AMPK bound to activator · the same entry in another collection · chain A against A, TM-score 1.00
- P54645 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase catalytic subunit… · a predicted model of the same protein · chain A against A, TM-score 0.99
- P80385 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase subunit gamma-1… · a predicted model of the same protein · chain C against A, TM-score 0.99
- P80386 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase subunit beta-1… · a predicted model of the same protein · chain B against A, TM-score 0.94
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P54645
- Every structure of UniProt P80386
- Every structure of UniProt P80385
- Elsewhere: RCSB PDB 6E4W · PDBe 6E4W · UniProt P54645 · UniProt P80386 · UniProt P80385
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